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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/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' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 0
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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) 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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ), 'gf_id' => 'HOM05D002579', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D002579' ), 'data_identifier' => 'HOM05D002579', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D002579', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '264', 'num_species' => '56' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia09814' => 'ach', 'Actinidia17786' => 'ach', 'Actinidia17787' => 'ach', 'Actinidia29534' => 'ach', 'Aqoxy6G01022' => 'aox', 'Aqoxy6G01023' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1P4JCB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1T1EY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6WE4S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VJY5J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91T88Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU5R1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VAK9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFD7CM' => 'arhy', 'ATR0820G012' => 'atr', 'ATR0820G067' => 'atr', 'ATR0820G269' => 'atr', 'ATR1090G001' => 'atr', 'CAN.G1215.5' => 'can', 'Ca_11501_v3' => 'car', 'Cc03_g11860' => 'ccan', 'Cc03_g11870' => 'ccan', 'Cc07_g16900' => 'ccan', 'Cc07_g16910' => 'ccan', 'Cc07_g16940' => 'ccan', 'Cc07_g16950' => 'ccan', 'Cc07_g16960' => 'ccan', 'Cc07_g17510' => 'ccan', 'Cc10_g14460' => 'ccan', 'Cc10_g14470' => 'ccan', 'Cc10_g14480' => 'ccan', 'Cc10_g14490' => 'ccan', 'Cc10_g14890' => 'ccan', 'Cfa002805' => 'cfa', 'Cfa018315' => 'cfa', 'Cfa018316' => 'cfa', 'Cfa018317' => 'cfa', 'Ciclev10003212m.g' => 'ccl', 'Ciclev10003278m.g' => 'ccl', 'Ciclev10026932m.g' => 'ccl', 'Ciclev10027409m.g' => 'ccl', 'Ciclev10027458m.g' => 'ccl', 'Ciclev10027490m.g' => 'ccl', 'CiPaw.01G080300' => 'cil', 'CiPaw.03G130400' => 'cil', 'CiPaw.04G087300' => 'cil', 'CiPaw.15G015300' => 'cil', 'COL.COLO4_22387' => 'col', 'COL.COLO4_22388' => 'col', 'COL.COLO4_22389' => 'col', 'COL.COLO4_22391' => 'col', 'COL.COLO4_22392' => 'col', 'COL.COLO4_29849' => 'col', 'COL.COLO4_29851' => 'col', 'COL.COLO4_29852' => 'col', 'COL.COLO4_34660' => 'col', 'CSS0018569' => 'camsi', 'CSS0023785' => 'camsi', 'CSS0026034' => 'camsi', 'CSS0040173' => 'camsi', 'CSS0044839' => 'camsi', 'DCAR_001410' => 'dca', 'DCAR_001411' => 'dca', 'DCAR_001412' => 'dca', 'DCAR_014355' => 'dca', 'DCAR_014356' => 'dca', 'DCAR_014357' => 'dca', 'DCAR_015333' => 'dca', 'Dinv00241' => 'din', 'Dinv14357' => 'din', 'Dinv14358' => 'din', 'Dinv25874' => 'din', 'Dinv25876' => 'din', 'Dinv41072' => 'din', 'Dinv41074' => 'din', 'Duzib116G0714' => 'dzi', 'Duzib147G0210' => 'dzi', 'Duzib147G1400' => 'dzi', 'Duzib264G0280' => 'dzi', 'Duzib264G0879' => 'dzi', 'ECA247G0005' => 'eca', 'Eucgr.F04231' => 'egr', 'Eucgr.F04233' => 'egr', 'Eucgr.I00276' => 'egr', 'Eucgr.I00277' => 'egr', 'Eucgr.I00279' => 'egr', 'Eucgr.I00280' => 'egr', 'Eucgr.I00281' => 'egr', 'Eucgr.I00282' => 'egr', 'Eucgr.I00283' => 'egr', 'Eucgr.I00284' => 'egr', 'FAN15G0025' => 'fan', 'FAN15G0316' => 'fan', 'FAN19G0470' => 'fan', 'FAN23G0132' => 'fan', 'FAN24G1474' => 'fan', 'FAN24G1714' => 'fan', 'FAN24G2874' => 'fan', 'FAN26G0592' => 'fan', 'FAN26G2798' => 'fan', 'FAN27G2054' => 'fan', 'FAN28G1212' => 'fan', 'FvH4_1g23820' => 'fve', 'FvH4_1g23821' => 'fve', 'FvH4_1g23860' => 'fve', 'FvH4_2g13510' => 'fve', 'FvH4_2g13513' => 'fve', 'FvH4_2g13520' => 'fve', 'FvH4_2g13550' => 'fve', 'Glyma.04G216900' => 'gma', 'Glyma.06G149080' => 'gma', 'Glyma.06G149120' => 'gma', 'Gohir.A02G137601' => 'ghi', 'Gohir.A05G270500' => 'ghi', 'Gohir.A05G270600' => 'ghi', 'Gohir.D03G048250' => 'ghi', 'Gohir.D05G272550' => 'ghi', 'Gohir.D05G272651' => 'ghi', 'Gorai.003G049500' => 'gra', 'Gorai.009G285600' => 'gra', 'Gorai.009G285700' => 'gra', 'GSVIVG01022287001' => 'vvi', 'GSVIVG01022288001' => 'vvi', 'GSVIVG01026633001' => 'vvi', 'GSVIVG01034545001' => 'vvi', 'HanXRQChr05g0161981' => 'han', 'HanXRQChr08g0218511' => 'han', 'HanXRQChr09g0272361' => 'han', 'HanXRQChr09g0272381' => 'han', 'HanXRQChr09g0272391' => 'han', 'HanXRQChr12g0374201' => 'han', 'HanXRQChr12g0374211' => 'han', 'HanXRQChr12g0378001' => 'han', 'HanXRQChr15g0483191' => 'han', 'Haze_17762' => 'cav', 'Haze_17765' => 'cav', 'HPP92_004412' => 'vpl', 'HPP92_004413' => 'vpl', 'HPP92_004414' => 'vpl', 'HPP92_004445' => 'vpl', 'Lj1g0010069' => 'lja', 'Lj1g0023003' => 'lja', 'Lj1g0027542' => 'lja', 'Lj2A586T27' => 'lonja', 'Lj2A588T34' => 'lonja', 'Lj2C586T7' => 'lonja', 'Lj2g0000381' => 'lja', 'Lj2g0021875' => 'lja', 'Lj4C697T11' => 'lonja', 'Lsat_1_v5_gn_3_64601' => 'lsa', 'Lsat_1_v5_gn_3_64621' => 'lsa', 'Lsat_1_v5_gn_3_64681' => 'lsa', 'Lsat_1_v5_gn_3_64721' => 'lsa', 'Lsat_1_v5_gn_6_100360' => 'lsa', 'Lsat_1_v5_gn_9_40981' => 'lsa', 'Lsat_1_v5_gn_9_41041' => 'lsa', 'Manes.13G081700' => 'mes', 'Manes.18G092900' => 'mes', 'MBI09_g06631_MAGBIO' => 'mbi', 'MBI09_g13937_MAGBIO' => 'mbi', 'MBI09_g22288_MAGBIO' => 'mbi', 'MBI09_g23421_MAGBIO' => 'mbi', 'MBI09_g30146_MAGBIO' => 'mbi', 'MBI09_g33103_MAGBIO' => 'mbi', 'MBI09_g39408_MAGBIO' => 'mbi', 'MBI09_g44121_MAGBIO' => 'mbi', 'MBI09_g47070_MAGBIO' => 'mbi', 'MBI09_g47071_MAGBIO' => 'mbi', 'MBI09_g47299_MAGBIO' => 'mbi', 'MBI09_g47616_MAGBIO' => 'mbi', 'MBI17_g24513_MAGBIO' => 'mbi', 'MBI17_g24514_MAGBIO' => 'mbi', 'MD05G1029900' => 'mdo', 'MD07G1183700' => 'mdo', 'MD10G1027700' => 'mdo', 'MD10G1027900' => 'mdo', 'MD10G1028300' => 'mdo', 'MD10G1030500' => 'mdo', 'MD10G1031000' => 'mdo', 'MD10G1031300' => 'mdo', 'MD15G1341000' => 'mdo', 'Medtr3g095340' => 'mtr', 'Medtr6g043700' => 'mtr', 'Migut.H02471' => 'egut', 'Nitab4.5_0002138g0100' => 'nta', 'Nn5g28764' => 'nnu', 'Oeu023260.1' => 'oeu', 'Oeu035197.1' => 'oeu', 'Oeu036101.1' => 'oeu', 'Oeu046044.1' => 'oeu', 'Os12g0165400' => 'osa', 'Os12g0166300' => 'osa', 'Os12g0170800' => 'osa', 'Peaxi162Scf00599g00213' => 'pax', 'Peaxi162Scf00599g00214' => 'pax', 'PGR044G0513' => 'pgr', 'PGR044G1268' => 'pgr', 'PGR044G2191' => 'pgr', 'PGR070G0001' => 'pgr', 'PGR070G0007' => 'pgr', 'PGR100G0001' => 'pgr', 'PGR100G0005' => 'pgr', 'PGR100G0009' => 'pgr', 'PGR119G1158' => 'pgr', 'PGR119G1278' => 'pgr', 'PGR119G1991' => 'pgr', 'PGSC0003DMG400003993' => 'stu', 'Phvul.009G146800' => 'pvu', 'Potri.001G306932' => 'ptr', 'Potri.001G307000' => 'ptr', 'Potri.001G307100' => 'ptr', 'Potri.002G067000' => 'ptr', 'Potri.005G193200' => 'ptr', 'Potri.019G002400' => 'ptr', 'Prupe.6G161900' => 'ppe', 'Prupe.8G032800' => 'ppe', 'Prupe.8G032900' => 'ppe', 'Prupe.8G033100' => 'ppe', 'Prupe.8G033300' => 'ppe', 'Psat2g116920' => 'psa', 'Psat2g182120' => 'psa', 'Psat5g064720' => 'psa', 'Psat5g064760' => 'psa', 'QL11p027658' => 'qlo', 'RcHm_v2.0_Chr2g0119701' => 'rch', 'RcHm_v2.0_Chr2g0119711' => 'rch', 'RcHm_v2.0_Chr2g0119741' => 'rch', 'RcHm_v2.0_Chr2g0119771' => 'rch', 'RcHm_v2.0_Chr2g0119811' => 'rch', 'RcHm_v2.0_Chr6g0275141' => 'rch', 'RcHm_v2.0_Chr6g0275151' => 'rch', 'RcHm_v2.0_Chr6g0275161' => 'rch', 'SEGI_03185' => 'sgi', 'SEGI_06234' => 'sgi', 'SEGI_09288' => 'sgi', 'SEGI_10474' => 'sgi', 'SEGI_12377' => 'sgi', 'SEGI_12470' => 'sgi', 'SEGI_13265' => 'sgi', 'SEGI_17175' => 'sgi', 'SEGI_20148' => 'sgi', 'SEGI_21769' => 'sgi', 'SEGI_26433' => 'sgi', 'SEGI_32426' => 'sgi', 'SEGI_35104' => 'sgi', 'SEGI_41540' => 'sgi', 'SMO365G0023' => 'smo', 'SMO365G0069' => 'smo', 'Solyc11g005480.2' => 'sly', 'Sopen11g001480' => 'spe', 'TAR381G0482' => 'tar', 'TAR381G1529' => 'tar', 'Thecc.01G118800' => 'tca', 'Thecc.01G119100' => 'tca', 'Thecc.01G119300' => 'tca', 'Thecc.08G154000' => 'tca', 'Thecc.08G154100' => 'tca', 'TPR.G18716' => 'tpr', 'TPR.G24439' => 'tpr', 'TPR.G6667' => 'tpr', 'TWI60G1367' => 'twi', 'TWI60G1421' => 'twi', 'VMungo1309G1278' => 'vmu', 'VMungo1309G2663' => 'vmu' ) $gf_id = 'HOM05D002579' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D002579' ) $data_identifier = 'HOM05D002579' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'atr' => (int) 4, 'can' => (int) 1, 'car' => (int) 1, 'ccan' => (int) 13, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 4, 'col' => (int) 9, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'egr' => (int) 10, 'fan' => (int) 11, 'fve' => (int) 7, 'gma' => (int) 3, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'vpl' => (int) 4, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 2, 'mbi' => (int) 14, 'mdo' => (int) 9, 'mtr' => (int) 2, 'egut' => (int) 1, 'nta' => (int) 1, 'nnu' => (int) 1, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 11, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'qlo' => (int) 1, 'rch' => (int) 8, 'sgi' => (int) 14, 'smo' => (int) 2, 'sly' => (int) 1, 'spe' => (int) 1, 'tar' => (int) 2, 'tca' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1309G2663' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1