If more than 50 genes/sequences are provided as input, then the associated running time can take some time. Therefore it is advisable to provide an email-address in case you are running the Interactive Phylogenetics Module with more than 50 genes. After processing you will be send an email with a link to the created phylogenetic tree.
The selection modi are exclusive: please choose either Gene selection or Species selection.
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 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'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 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'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE 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'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_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' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 'FAN07G2626' => 'fan', 'FAN07G2652' => 'fan', 'FAN07G2662' => 'fan', 'FAN08G0470' => 'fan', 'FAN08G0594' => 'fan', 'FAN08G0741' => 'fan', 'FAN08G0756' => 'fan', 'FAN08G0792' => 'fan', 'FAN08G0912' => 'fan', 'FAN08G0924' => 'fan', 'FAN08G0957' => 'fan', 'FAN08G1091' => 'fan', 'FAN08G1171' => 'fan', 'FAN08G1534' => 'fan', 'FAN08G2520' => 'fan', 'FAN08G2830' => 'fan', 'FAN08G3124' => 'fan', 'FAN09G0396' => 'fan', 'FAN09G0803' => 'fan', 'FAN09G1250' => 'fan', 'FAN09G1466' => 'fan', 'FAN09G1703' => 'fan', 'FAN09G2002' => 'fan', 'FAN09G2116' => 'fan', 'FAN09G2422' => 'fan', 'FAN09G3190' => 'fan', 'FAN10G2722' => 'fan', 'FAN10G2869' => 'fan', 'FAN10G3055' => 'fan', 'FAN10G3245' => 'fan', 'FAN10G4175' => 'fan', 'FAN11G1591' => 'fan', 'FAN11G1756' => 'fan', 'FAN11G3491' => 'fan', 'FAN13G1226' => 'fan', 'FAN13G1743' => 'fan', 'FAN15G0260' => 'fan', 'FAN15G0452' => 'fan', 'FAN15G0787' => 'fan', 'FAN15G1040' => 'fan', 'FAN15G2098' => 'fan', 'FAN15G2254' => 'fan', 'FAN15G3269' => 'fan', 'FAN15G3418' => 'fan', 'FAN15G3655' => 'fan', 'FAN16G0065' => 'fan', 'FAN16G0241' => 'fan', 'FAN16G0854' => 'fan', 'FAN16G1106' => 'fan', 'FAN16G1119' => 'fan', 'FAN16G1239' => 'fan', 'FAN16G1333' => 'fan', 'FAN16G1582' => 'fan', 'FAN16G1628' => 'fan', 'FAN16G1736' => 'fan', 'FAN16G1972' => 'fan', 'FAN16G2151' => 'fan', 'FAN16G2630' => 'fan', 'FAN16G3591' => 'fan', 'FAN16G3743' => 'fan', 'FAN17G0056' => 'fan', 'FAN17G0116' => 'fan', 'FAN17G0162' => 'fan', 'FAN17G0461' => 'fan', 'FAN17G0832' => 'fan', 'FAN17G0994' => 'fan', 'FAN17G1142' => 'fan', 'FAN17G1746' => 'fan', 'FAN17G1918' => 'fan', 'FAN17G2316' => 'fan', 'FAN17G2788' => 'fan', 'FAN17G2945' => 'fan', 'FAN20G1178' => 'fan', 'FAN20G1210' => 'fan', 'FAN20G1437' => 'fan', 'FAN20G1567' => 'fan', 'FAN20G2716' => 'fan', 'FAN21G0091' => 'fan', 'FAN21G0166' => 'fan', 'FAN21G0446' => 'fan', 'FAN21G0465' => 'fan', 'FAN21G0715' => 'fan', 'FAN21G0867' => 'fan', 'FAN21G1115' => 'fan', 'FAN21G1141' => 'fan', 'FAN21G1418' => 'fan', 'FAN21G1914' => 'fan', 'FAN21G2045' => 'fan', 'FAN21G2196' => 'fan', 'FAN21G2320' => 'fan', 'FAN21G2621' => 'fan', 'FAN21G3451' => 'fan', 'FAN21G3797' => 'fan', 'FAN22G0041' => 'fan', 'FAN22G0105' => 'fan', 'FAN22G0521' => 'fan', 'FAN22G0637' => 'fan', 'FAN22G0912' => 'fan', 'FAN22G1007' => 'fan', 'FAN22G1478' => 'fan', 'FAN22G1934' => 'fan', 'FAN23G0027' => 'fan', 'FAN23G0084' => 'fan', 'FAN23G0574' => 'fan', 'FAN23G0642' => 'fan', 'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 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'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 0
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 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'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 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'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 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'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 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'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 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=> 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 'FAN07G2626' => 'fan', 'FAN07G2652' => 'fan', 'FAN07G2662' => 'fan', 'FAN08G0470' => 'fan', 'FAN08G0594' => 'fan', 'FAN08G0741' => 'fan', 'FAN08G0756' => 'fan', 'FAN08G0792' => 'fan', 'FAN08G0912' => 'fan', 'FAN08G0924' => 'fan', 'FAN08G0957' => 'fan', 'FAN08G1091' => 'fan', 'FAN08G1171' => 'fan', 'FAN08G1534' => 'fan', 'FAN08G2520' => 'fan', 'FAN08G2830' => 'fan', 'FAN08G3124' => 'fan', 'FAN09G0396' => 'fan', 'FAN09G0803' => 'fan', 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'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 'FAN07G2626' => 'fan', 'FAN07G2652' => 'fan', 'FAN07G2662' => 'fan', 'FAN08G0470' => 'fan', 'FAN08G0594' => 'fan', 'FAN08G0741' => 'fan', 'FAN08G0756' => 'fan', 'FAN08G0792' => 'fan', 'FAN08G0912' => 'fan', 'FAN08G0924' => 'fan', 'FAN08G0957' => 'fan', 'FAN08G1091' => 'fan', 'FAN08G1171' => 'fan', 'FAN08G1534' => 'fan', 'FAN08G2520' => 'fan', 'FAN08G2830' => 'fan', 'FAN08G3124' => 'fan', 'FAN09G0396' => 'fan', 'FAN09G0803' => 'fan', 'FAN09G1250' => 'fan', 'FAN09G1466' => 'fan', 'FAN09G1703' => 'fan', 'FAN09G2002' => 'fan', 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'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 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'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 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'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 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'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' 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'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 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'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 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'FAN21G1914' => 'fan', 'FAN21G2045' => 'fan', 'FAN21G2196' => 'fan', 'FAN21G2320' => 'fan', 'FAN21G2621' => 'fan', 'FAN21G3451' => 'fan', 'FAN21G3797' => 'fan', 'FAN22G0041' => 'fan', 'FAN22G0105' => 'fan', 'FAN22G0521' => 'fan', 'FAN22G0637' => 'fan', 'FAN22G0912' => 'fan', 'FAN22G1007' => 'fan', 'FAN22G1478' => 'fan', 'FAN22G1934' => 'fan', 'FAN23G0027' => 'fan', 'FAN23G0084' => 'fan', 'FAN23G0574' => 'fan', 'FAN23G0642' => 'fan', 'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 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'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' 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'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 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'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 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'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' 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'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 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'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 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'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 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'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 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'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 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'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 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'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 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'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 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'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 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=> 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 'FAN07G2626' => 'fan', 'FAN07G2652' => 'fan', 'FAN07G2662' => 'fan', 'FAN08G0470' => 'fan', 'FAN08G0594' => 'fan', 'FAN08G0741' => 'fan', 'FAN08G0756' => 'fan', 'FAN08G0792' => 'fan', 'FAN08G0912' => 'fan', 'FAN08G0924' => 'fan', 'FAN08G0957' => 'fan', 'FAN08G1091' => 'fan', 'FAN08G1171' => 'fan', 'FAN08G1534' => 'fan', 'FAN08G2520' => 'fan', 'FAN08G2830' => 'fan', 'FAN08G3124' => 'fan', 'FAN09G0396' => 'fan', 'FAN09G0803' => 'fan', 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'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 'FAN07G2626' => 'fan', 'FAN07G2652' => 'fan', 'FAN07G2662' => 'fan', 'FAN08G0470' => 'fan', 'FAN08G0594' => 'fan', 'FAN08G0741' => 'fan', 'FAN08G0756' => 'fan', 'FAN08G0792' => 'fan', 'FAN08G0912' => 'fan', 'FAN08G0924' => 'fan', 'FAN08G0957' => 'fan', 'FAN08G1091' => 'fan', 'FAN08G1171' => 'fan', 'FAN08G1534' => 'fan', 'FAN08G2520' => 'fan', 'FAN08G2830' => 'fan', 'FAN08G3124' => 'fan', 'FAN09G0396' => 'fan', 'FAN09G0803' => 'fan', 'FAN09G1250' => 'fan', 'FAN09G1466' => 'fan', 'FAN09G1703' => 'fan', 'FAN09G2002' => 'fan', 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'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 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'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 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'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 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'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' 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'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 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'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 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'FAN21G1914' => 'fan', 'FAN21G2045' => 'fan', 'FAN21G2196' => 'fan', 'FAN21G2320' => 'fan', 'FAN21G2621' => 'fan', 'FAN21G3451' => 'fan', 'FAN21G3797' => 'fan', 'FAN22G0041' => 'fan', 'FAN22G0105' => 'fan', 'FAN22G0521' => 'fan', 'FAN22G0637' => 'fan', 'FAN22G0912' => 'fan', 'FAN22G1007' => 'fan', 'FAN22G1478' => 'fan', 'FAN22G1934' => 'fan', 'FAN23G0027' => 'fan', 'FAN23G0084' => 'fan', 'FAN23G0574' => 'fan', 'FAN23G0642' => 'fan', 'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 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'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' 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'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 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'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 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'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' 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'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 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'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 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'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 'FAN07G2626' => 'fan', 'FAN07G2652' => 'fan', 'FAN07G2662' => 'fan', 'FAN08G0470' => 'fan', 'FAN08G0594' => 'fan', 'FAN08G0741' => 'fan', 'FAN08G0756' => 'fan', 'FAN08G0792' => 'fan', 'FAN08G0912' => 'fan', 'FAN08G0924' => 'fan', 'FAN08G0957' => 'fan', 'FAN08G1091' => 'fan', 'FAN08G1171' => 'fan', 'FAN08G1534' => 'fan', 'FAN08G2520' => 'fan', 'FAN08G2830' => 'fan', 'FAN08G3124' => 'fan', 'FAN09G0396' => 'fan', 'FAN09G0803' => 'fan', 'FAN09G1250' => 'fan', 'FAN09G1466' => 'fan', 'FAN09G1703' => 'fan', 'FAN09G2002' => 'fan', 'FAN09G2116' => 'fan', 'FAN09G2422' => 'fan', 'FAN09G3190' => 'fan', 'FAN10G2722' => 'fan', 'FAN10G2869' => 'fan', 'FAN10G3055' => 'fan', 'FAN10G3245' => 'fan', 'FAN10G4175' => 'fan', 'FAN11G1591' => 'fan', 'FAN11G1756' => 'fan', 'FAN11G3491' => 'fan', 'FAN13G1226' => 'fan', 'FAN13G1743' => 'fan', 'FAN15G0260' => 'fan', 'FAN15G0452' => 'fan', 'FAN15G0787' => 'fan', 'FAN15G1040' => 'fan', 'FAN15G2098' => 'fan', 'FAN15G2254' => 'fan', 'FAN15G3269' => 'fan', 'FAN15G3418' => 'fan', 'FAN15G3655' => 'fan', 'FAN16G0065' => 'fan', 'FAN16G0241' => 'fan', 'FAN16G0854' => 'fan', 'FAN16G1106' => 'fan', 'FAN16G1119' => 'fan', 'FAN16G1239' => 'fan', 'FAN16G1333' => 'fan', 'FAN16G1582' => 'fan', 'FAN16G1628' => 'fan', 'FAN16G1736' => 'fan', 'FAN16G1972' => 'fan', 'FAN16G2151' => 'fan', 'FAN16G2630' => 'fan', 'FAN16G3591' => 'fan', 'FAN16G3743' => 'fan', 'FAN17G0056' => 'fan', 'FAN17G0116' => 'fan', 'FAN17G0162' => 'fan', 'FAN17G0461' => 'fan', 'FAN17G0832' => 'fan', 'FAN17G0994' => 'fan', 'FAN17G1142' => 'fan', 'FAN17G1746' => 'fan', 'FAN17G1918' => 'fan', 'FAN17G2316' => 'fan', 'FAN17G2788' => 'fan', 'FAN17G2945' => 'fan', 'FAN20G1178' => 'fan', 'FAN20G1210' => 'fan', 'FAN20G1437' => 'fan', 'FAN20G1567' => 'fan', 'FAN20G2716' => 'fan', 'FAN21G0091' => 'fan', 'FAN21G0166' => 'fan', 'FAN21G0446' => 'fan', 'FAN21G0465' => 'fan', 'FAN21G0715' => 'fan', 'FAN21G0867' => 'fan', 'FAN21G1115' => 'fan', 'FAN21G1141' => 'fan', 'FAN21G1418' => 'fan', 'FAN21G1914' => 'fan', 'FAN21G2045' => 'fan', 'FAN21G2196' => 'fan', 'FAN21G2320' => 'fan', 'FAN21G2621' => 'fan', 'FAN21G3451' => 'fan', 'FAN21G3797' => 'fan', 'FAN22G0041' => 'fan', 'FAN22G0105' => 'fan', 'FAN22G0521' => 'fan', 'FAN22G0637' => 'fan', 'FAN22G0912' => 'fan', 'FAN22G1007' => 'fan', 'FAN22G1478' => 'fan', 'FAN22G1934' => 'fan', 'FAN23G0027' => 'fan', 'FAN23G0084' => 'fan', 'FAN23G0574' => 'fan', 'FAN23G0642' => 'fan', 'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 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'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 'FAN07G2626' => 'fan', 'FAN07G2652' => 'fan', 'FAN07G2662' => 'fan', 'FAN08G0470' => 'fan', 'FAN08G0594' => 'fan', 'FAN08G0741' => 'fan', 'FAN08G0756' => 'fan', 'FAN08G0792' => 'fan', 'FAN08G0912' => 'fan', 'FAN08G0924' => 'fan', 'FAN08G0957' => 'fan', 'FAN08G1091' => 'fan', 'FAN08G1171' => 'fan', 'FAN08G1534' => 'fan', 'FAN08G2520' => 'fan', 'FAN08G2830' => 'fan', 'FAN08G3124' => 'fan', 'FAN09G0396' => 'fan', 'FAN09G0803' => 'fan', 'FAN09G1250' => 'fan', 'FAN09G1466' => 'fan', 'FAN09G1703' => 'fan', 'FAN09G2002' => 'fan', 'FAN09G2116' => 'fan', 'FAN09G2422' => 'fan', 'FAN09G3190' => 'fan', 'FAN10G2722' => 'fan', 'FAN10G2869' => 'fan', 'FAN10G3055' => 'fan', 'FAN10G3245' => 'fan', 'FAN10G4175' => 'fan', 'FAN11G1591' => 'fan', 'FAN11G1756' => 'fan', 'FAN11G3491' => 'fan', 'FAN13G1226' => 'fan', 'FAN13G1743' => 'fan', 'FAN15G0260' => 'fan', 'FAN15G0452' => 'fan', 'FAN15G0787' => 'fan', 'FAN15G1040' => 'fan', 'FAN15G2098' => 'fan', 'FAN15G2254' => 'fan', 'FAN15G3269' => 'fan', 'FAN15G3418' => 'fan', 'FAN15G3655' => 'fan', 'FAN16G0065' => 'fan', 'FAN16G0241' => 'fan', 'FAN16G0854' => 'fan', 'FAN16G1106' => 'fan', 'FAN16G1119' => 'fan', 'FAN16G1239' => 'fan', 'FAN16G1333' => 'fan', 'FAN16G1582' => 'fan', 'FAN16G1628' => 'fan', 'FAN16G1736' => 'fan', 'FAN16G1972' => 'fan', 'FAN16G2151' => 'fan', 'FAN16G2630' => 'fan', 'FAN16G3591' => 'fan', 'FAN16G3743' => 'fan', 'FAN17G0056' => 'fan', 'FAN17G0116' => 'fan', 'FAN17G0162' => 'fan', 'FAN17G0461' => 'fan', 'FAN17G0832' => 'fan', 'FAN17G0994' => 'fan', 'FAN17G1142' => 'fan', 'FAN17G1746' => 'fan', 'FAN17G1918' => 'fan', 'FAN17G2316' => 'fan', 'FAN17G2788' => 'fan', 'FAN17G2945' => 'fan', 'FAN20G1178' => 'fan', 'FAN20G1210' => 'fan', 'FAN20G1437' => 'fan', 'FAN20G1567' => 'fan', 'FAN20G2716' => 'fan', 'FAN21G0091' => 'fan', 'FAN21G0166' => 'fan', 'FAN21G0446' => 'fan', 'FAN21G0465' => 'fan', 'FAN21G0715' => 'fan', 'FAN21G0867' => 'fan', 'FAN21G1115' => 'fan', 'FAN21G1141' => 'fan', 'FAN21G1418' => 'fan', 'FAN21G1914' => 'fan', 'FAN21G2045' => 'fan', 'FAN21G2196' => 'fan', 'FAN21G2320' => 'fan', 'FAN21G2621' => 'fan', 'FAN21G3451' => 'fan', 'FAN21G3797' => 'fan', 'FAN22G0041' => 'fan', 'FAN22G0105' => 'fan', 'FAN22G0521' => 'fan', 'FAN22G0637' => 'fan', 'FAN22G0912' => 'fan', 'FAN22G1007' => 'fan', 'FAN22G1478' => 'fan', 'FAN22G1934' => 'fan', 'FAN23G0027' => 'fan', 'FAN23G0084' => 'fan', 'FAN23G0574' => 'fan', 'FAN23G0642' => 'fan', 'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 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'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 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'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 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'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 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=> 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 'FAN07G2626' => 'fan', 'FAN07G2652' => 'fan', 'FAN07G2662' => 'fan', 'FAN08G0470' => 'fan', 'FAN08G0594' => 'fan', 'FAN08G0741' => 'fan', 'FAN08G0756' => 'fan', 'FAN08G0792' => 'fan', 'FAN08G0912' => 'fan', 'FAN08G0924' => 'fan', 'FAN08G0957' => 'fan', 'FAN08G1091' => 'fan', 'FAN08G1171' => 'fan', 'FAN08G1534' => 'fan', 'FAN08G2520' => 'fan', 'FAN08G2830' => 'fan', 'FAN08G3124' => 'fan', 'FAN09G0396' => 'fan', 'FAN09G0803' => 'fan', 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'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 'FAN07G2626' => 'fan', 'FAN07G2652' => 'fan', 'FAN07G2662' => 'fan', 'FAN08G0470' => 'fan', 'FAN08G0594' => 'fan', 'FAN08G0741' => 'fan', 'FAN08G0756' => 'fan', 'FAN08G0792' => 'fan', 'FAN08G0912' => 'fan', 'FAN08G0924' => 'fan', 'FAN08G0957' => 'fan', 'FAN08G1091' => 'fan', 'FAN08G1171' => 'fan', 'FAN08G1534' => 'fan', 'FAN08G2520' => 'fan', 'FAN08G2830' => 'fan', 'FAN08G3124' => 'fan', 'FAN09G0396' => 'fan', 'FAN09G0803' => 'fan', 'FAN09G1250' => 'fan', 'FAN09G1466' => 'fan', 'FAN09G1703' => 'fan', 'FAN09G2002' => 'fan', 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'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 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'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 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'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 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'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' 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'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 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'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 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'FAN21G1914' => 'fan', 'FAN21G2045' => 'fan', 'FAN21G2196' => 'fan', 'FAN21G2320' => 'fan', 'FAN21G2621' => 'fan', 'FAN21G3451' => 'fan', 'FAN21G3797' => 'fan', 'FAN22G0041' => 'fan', 'FAN22G0105' => 'fan', 'FAN22G0521' => 'fan', 'FAN22G0637' => 'fan', 'FAN22G0912' => 'fan', 'FAN22G1007' => 'fan', 'FAN22G1478' => 'fan', 'FAN22G1934' => 'fan', 'FAN23G0027' => 'fan', 'FAN23G0084' => 'fan', 'FAN23G0574' => 'fan', 'FAN23G0642' => 'fan', 'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 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'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' 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'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 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'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 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'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' 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'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 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'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 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'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 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'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 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'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 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'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 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'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 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'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 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'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 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=> 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 'FAN07G2626' => 'fan', 'FAN07G2652' => 'fan', 'FAN07G2662' => 'fan', 'FAN08G0470' => 'fan', 'FAN08G0594' => 'fan', 'FAN08G0741' => 'fan', 'FAN08G0756' => 'fan', 'FAN08G0792' => 'fan', 'FAN08G0912' => 'fan', 'FAN08G0924' => 'fan', 'FAN08G0957' => 'fan', 'FAN08G1091' => 'fan', 'FAN08G1171' => 'fan', 'FAN08G1534' => 'fan', 'FAN08G2520' => 'fan', 'FAN08G2830' => 'fan', 'FAN08G3124' => 'fan', 'FAN09G0396' => 'fan', 'FAN09G0803' => 'fan', 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'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 'FAN07G2626' => 'fan', 'FAN07G2652' => 'fan', 'FAN07G2662' => 'fan', 'FAN08G0470' => 'fan', 'FAN08G0594' => 'fan', 'FAN08G0741' => 'fan', 'FAN08G0756' => 'fan', 'FAN08G0792' => 'fan', 'FAN08G0912' => 'fan', 'FAN08G0924' => 'fan', 'FAN08G0957' => 'fan', 'FAN08G1091' => 'fan', 'FAN08G1171' => 'fan', 'FAN08G1534' => 'fan', 'FAN08G2520' => 'fan', 'FAN08G2830' => 'fan', 'FAN08G3124' => 'fan', 'FAN09G0396' => 'fan', 'FAN09G0803' => 'fan', 'FAN09G1250' => 'fan', 'FAN09G1466' => 'fan', 'FAN09G1703' => 'fan', 'FAN09G2002' => 'fan', 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'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 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'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 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'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 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'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' 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'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 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'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 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'FAN21G1914' => 'fan', 'FAN21G2045' => 'fan', 'FAN21G2196' => 'fan', 'FAN21G2320' => 'fan', 'FAN21G2621' => 'fan', 'FAN21G3451' => 'fan', 'FAN21G3797' => 'fan', 'FAN22G0041' => 'fan', 'FAN22G0105' => 'fan', 'FAN22G0521' => 'fan', 'FAN22G0637' => 'fan', 'FAN22G0912' => 'fan', 'FAN22G1007' => 'fan', 'FAN22G1478' => 'fan', 'FAN22G1934' => 'fan', 'FAN23G0027' => 'fan', 'FAN23G0084' => 'fan', 'FAN23G0574' => 'fan', 'FAN23G0642' => 'fan', 'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 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'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' 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'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 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'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 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'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' 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'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 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'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 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'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 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'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 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'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 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'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 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'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 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'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 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'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 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=> 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 'FAN07G2626' => 'fan', 'FAN07G2652' => 'fan', 'FAN07G2662' => 'fan', 'FAN08G0470' => 'fan', 'FAN08G0594' => 'fan', 'FAN08G0741' => 'fan', 'FAN08G0756' => 'fan', 'FAN08G0792' => 'fan', 'FAN08G0912' => 'fan', 'FAN08G0924' => 'fan', 'FAN08G0957' => 'fan', 'FAN08G1091' => 'fan', 'FAN08G1171' => 'fan', 'FAN08G1534' => 'fan', 'FAN08G2520' => 'fan', 'FAN08G2830' => 'fan', 'FAN08G3124' => 'fan', 'FAN09G0396' => 'fan', 'FAN09G0803' => 'fan', 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'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 'FAN07G2626' => 'fan', 'FAN07G2652' => 'fan', 'FAN07G2662' => 'fan', 'FAN08G0470' => 'fan', 'FAN08G0594' => 'fan', 'FAN08G0741' => 'fan', 'FAN08G0756' => 'fan', 'FAN08G0792' => 'fan', 'FAN08G0912' => 'fan', 'FAN08G0924' => 'fan', 'FAN08G0957' => 'fan', 'FAN08G1091' => 'fan', 'FAN08G1171' => 'fan', 'FAN08G1534' => 'fan', 'FAN08G2520' => 'fan', 'FAN08G2830' => 'fan', 'FAN08G3124' => 'fan', 'FAN09G0396' => 'fan', 'FAN09G0803' => 'fan', 'FAN09G1250' => 'fan', 'FAN09G1466' => 'fan', 'FAN09G1703' => 'fan', 'FAN09G2002' => 'fan', 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'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 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'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 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'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 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'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' 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'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 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'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 'FAN04G2893' => 'fan', 'FAN04G2940' => 'fan', 'FAN04G3055' => 'fan', 'FAN05G0364' => 'fan', 'FAN05G1077' => 'fan', 'FAN05G1213' => 'fan', 'FAN05G1283' => 'fan', 'FAN05G1467' => 'fan', 'FAN05G1521' => 'fan', 'FAN05G1684' => 'fan', 'FAN05G1917' => 'fan', 'FAN05G2274' => 'fan', 'FAN05G2470' => 'fan', 'FAN05G2498' => 'fan', 'FAN05G2505' => 'fan', 'FAN05G2710' => 'fan', 'FAN05G2863' => 'fan', 'FAN05G2969' => 'fan', 'FAN05G3337' => 'fan', 'FAN05G3670' => 'fan', 'FAN05G3713' => 'fan', 'FAN05G4002' => 'fan', 'FAN05G4129' => 'fan', 'FAN05G4558' => 'fan', 'FAN07G0008' => 'fan', 'FAN07G0198' => 'fan', 'FAN07G0199' => 'fan', 'FAN07G0250' => 'fan', 'FAN07G0415' => 'fan', 'FAN07G0599' => 'fan', 'FAN07G0619' => 'fan', 'FAN07G1188' => 'fan', 'FAN07G1360' => 'fan', 'FAN07G1407' => 'fan', 'FAN07G1411' => 'fan', 'FAN07G1644' => 'fan', 'FAN07G1676' => 'fan', 'FAN07G1737' => 'fan', 'FAN07G1759' => 'fan', 'FAN07G1874' => 'fan', 'FAN07G2010' => 'fan', 'FAN07G2213' => 'fan', 'FAN07G2361' => 'fan', 'FAN07G2512' => 'fan', 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'FAN21G1914' => 'fan', 'FAN21G2045' => 'fan', 'FAN21G2196' => 'fan', 'FAN21G2320' => 'fan', 'FAN21G2621' => 'fan', 'FAN21G3451' => 'fan', 'FAN21G3797' => 'fan', 'FAN22G0041' => 'fan', 'FAN22G0105' => 'fan', 'FAN22G0521' => 'fan', 'FAN22G0637' => 'fan', 'FAN22G0912' => 'fan', 'FAN22G1007' => 'fan', 'FAN22G1478' => 'fan', 'FAN22G1934' => 'fan', 'FAN23G0027' => 'fan', 'FAN23G0084' => 'fan', 'FAN23G0574' => 'fan', 'FAN23G0642' => 'fan', 'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 'cme', 'MELO3C020727.2' => 'cme', 'MELO3C024966.2' => 'cme', 'MELO3C025089.2' => 'cme', 'MELO3C025186.2' => 'cme', 'MELO3C025271.2' => 'cme', 'MELO3C026674.2' => 'cme', 'MELO3C027164.2' => 'cme', 'MELO3C027233.2' => 'cme', 'MELO3C027312.2' => 'cme', 'MELO3C027374.2' => 'cme', 'MELO3C027378.2' => 'cme', 'MELO3C027383.2' => 'cme', 'MELO3C027457.2' => 'cme', 'MELO3C027458.2' => 'cme', 'MELO3C027499.2' => 'cme', 'MELO3C027500.2' => 'cme', 'MELO3C027503.2' => 'cme', 'MELO3C027512.2' => 'cme', 'MELO3C027513.2' => 'cme', 'MELO3C027708.2' => 'cme', 'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' => 'fan', 'FAN02G3163' => 'fan', 'FAN02G3174' => 'fan', 'FAN02G3458' => 'fan', 'FAN02G3797' => 'fan', 'FAN02G4026' => 'fan', 'FAN02G4191' => 'fan', 'FAN03G0379' => 'fan', 'FAN03G0592' => 'fan', 'FAN03G0692' => 'fan', 'FAN03G1414' => 'fan', 'FAN03G1518' => 'fan', 'FAN03G1525' => 'fan', 'FAN03G1614' => 'fan', 'FAN03G1964' => 'fan', 'FAN03G2153' => 'fan', 'FAN03G2265' => 'fan', 'FAN03G2545' => 'fan', 'FAN03G2630' => 'fan', 'FAN03G3450' => 'fan', 'FAN04G0230' => 'fan', 'FAN04G0414' => 'fan', 'FAN04G1934' => 'fan', 'FAN04G2697' => 'fan', 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'MELO3C027709.2' => 'cme', 'MELO3C028822.2' => 'cme', 'MELO3C028824.2' => 'cme', 'MELO3C028888.2' => 'cme', 'MELO3C029387.2' => 'cme', 'MELO3C029460.2' => 'cme', 'MELO3C029462.2' => 'cme', 'MELO3C029552.2' => 'cme', 'MELO3C029899.2' => 'cme', 'MELO3C030397.2' => 'cme', 'MELO3C030571.2' => 'cme', 'MELO3C030623.2' => 'cme', 'MELO3C031150.2' => 'cme', 'MELO3C031252.2' => 'cme', 'MELO3C031922.2' => 'cme', 'MELO3C032430.2' => 'cme', 'MELO3C032455.2' => 'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 'cla', 'ClCG02G008520' => 'cla', 'ClCG02G008620' => 'cla', 'ClCG02G008670' => 'cla', 'ClCG02G010500' => 'cla', 'ClCG02G011030' => 'cla', 'ClCG02G011040' => 'cla', 'ClCG03G010460' => 'cla', 'ClCG03G010780' => 'cla', 'ClCG04G001610' => 'cla', 'ClCG04G004480' => 'cla', 'ClCG05G012940' => 'cla', 'ClCG06G010440' => 'cla', 'ClCG07G001540' => 'cla', 'ClCG07G007890' => 'cla', 'ClCG07G009260' => 'cla', 'ClCG07G009270' => 'cla', 'ClCG08G000680' => 'cla', 'ClCG08G001070' => 'cla', 'ClCG08G006380' => 'cla', 'ClCG09G009920' => 'cla', 'ClCG09G014960' => 'cla', 'ClCG10G005780' => 'cla', 'ClCG10G007940' => 'cla', 'ClCG10G010700' => 'cla', 'ClCG10G011550' => 'cla', 'ClCG10G015790' => 'cla', 'ClCG11G010690' => 'cla', 'ClCG11G011320' => 'cla', 'CsaV3_7G018370' => 'csa', 'CSS0000857' => 'camsi', 'CSS0009665' => 'camsi', 'CSS0011934' => 'camsi', 'CSS0012545' => 'camsi', 'CSS0025200' => 'camsi', 'CSS0029427' => 'camsi', 'CSS0033910' => 'camsi', 'Dinv29064' => 'din', 'EL10Ac1g00951' => 'bvu', 'EL10Ac1g01776' => 'bvu', 'EL10Ac1g01780' => 'bvu', 'EL10Ac1g02017' => 'bvu', 'EL10Ac2g03094' => 'bvu', 'EL10Ac2g03232' => 'bvu', 'EL10Ac3g05450' => 'bvu', 'EL10Ac3g06176' => 'bvu', 'EL10Ac4g08194' => 'bvu', 'EL10Ac4g08443' => 'bvu', 'EL10Ac4g08691' => 'bvu', 'EL10Ac5g11547' => 'bvu', 'EL10Ac5g11830' => 'bvu', 'EL10Ac5g11925' => 'bvu', 'EL10Ac6g13854' => 'bvu', 'EL10Ac6g14340' => 'bvu', 'EL10Ac6g15005' => 'bvu', 'EL10Ac7g17363' => 'bvu', 'EL10Ac7g17728' => 'bvu', 'EL10Ac7g17946' => 'bvu', 'EL10Ac7g17947' => 'bvu', 'EL10Ac8g19601' => 'bvu', 'EL10Ac8g19639' => 'bvu', 'EL10Ac8g19640' => 'bvu', 'EL10As14g24088' => 'bvu', 'EL10As7g23760' => 'bvu', 'FAN02G0009' => 'fan', 'FAN02G0708' => 'fan', 'FAN02G1269' => 'fan', 'FAN02G1939' => 'fan', 'FAN02G1977' => 'fan', 'FAN02G2053' => 'fan', 'FAN02G2361' => 'fan', 'FAN02G2455' => 'fan', 'FAN02G2681' => 'fan', 'FAN02G2779' => 'fan', 'FAN02G3066' => 'fan', 'FAN02G3111' 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'FAN23G1134' => 'fan', 'FAN23G1277' => 'fan', 'FAN23G1287' => 'fan', 'FAN23G1299' => 'fan', 'FAN23G1565' => 'fan', 'FAN23G1829' => 'fan', 'FAN23G1888' => 'fan', 'FAN23G1928' => 'fan', 'FAN23G2327' => 'fan', 'FAN23G2347' => 'fan', 'FAN23G2410' => 'fan', 'FAN23G2831' => 'fan', 'FAN23G3071' => 'fan', 'FAN24G0535' => 'fan', 'FAN24G0600' => 'fan', 'FAN25G0179' => 'fan', 'FAN25G0467' => 'fan', 'FAN25G0906' => 'fan', 'FAN25G0961' => 'fan', 'FAN25G1897' => 'fan', 'FAN25G2497' => 'fan', 'FAN25G2617' => 'fan', 'FAN25G3247' => 'fan', 'FAN25G3516' => 'fan', 'FAN25G3580' => 'fan', 'FAN25G3760' => 'fan', 'FAN26G0214' => 'fan', 'FAN26G0298' => 'fan', 'FAN26G0419' => 'fan', 'FAN26G0507' => 'fan', 'FAN26G0586' => 'fan', 'FAN26G0680' => 'fan', 'FAN26G0766' => 'fan', 'FAN26G0822' => 'fan', 'FAN26G0848' => 'fan', 'FAN26G0852' => 'fan', 'FAN26G0976' => 'fan', 'FAN26G1098' => 'fan', 'FAN26G1105' => 'fan', 'FAN26G1142' => 'fan', 'FAN26G1272' => 'fan', 'FAN26G1328' => 'fan', 'FAN26G1363' => 'fan', 'FAN26G1475' => 'fan', 'FAN26G1552' => 'fan', 'FAN26G1666' => 'fan', 'FAN26G1678' => 'fan', 'FAN26G2145' => 'fan', 'FAN26G2429' => 'fan', 'FAN26G2544' => 'fan', 'FAN26G2722' => 'fan', 'FAN26G2784' => 'fan', 'FAN27G1182' => 'fan', 'FAN27G1552' => 'fan', 'FAN27G1818' => 'fan', 'FAN27G2744' => 'fan', 'FAN28G0349' => 'fan', 'FAN28G0594' => 'fan', 'FAN28G0858' => 'fan', 'FAN28G1060' => 'fan', 'FAN28G1306' => 'fan', 'FAN28G1923' => 'fan', 'FAN28G2071' => 'fan', 'FAN28G2204' => 'fan', 'FAN28G2412' => 'fan', 'FAN28G2850' => 'fan', 'FvH4_1g18561' => 'fve', 'FvH4_1g29681' => 'fve', 'FvH4_2g15190' => 'fve', 'FvH4_3g22800' => 'fve', 'FvH4_3g22801' => 'fve', 'FvH4_3g26700' => 'fve', 'FvH4_4g15162' => 'fve', 'FvH4_4g15163' => 'fve', 'FvH4_4g15164' => 'fve', 'FvH4_4g22273' => 'fve', 'FvH4_7g03670' => 'fve', 'FvH4_7g03671' => 'fve', 'Hma1.2p1_0017F.1_g011210' => 'hma', 'Hma1.2p1_0120F.1_g057263' => 'hma', 'Hma1.2p1_0161F.1_g071390' => 'hma', 'Hma1.2p1_0446F.1_g154720' => 'hma', 'Hma1.2p1_0494F.1_g165370' => 'hma', 'Hma1.2p1_0663F.1_g198890' => 'hma', 'Hma1.2p1_0663F.1_g198895' => 'hma', 'Hma1.2p1_0901F.1_g234680' => 'hma', 'Hma1.2p1_1168F.1_g263170' => 'hma', 'Hma1.2p1_1193F.1_g265550' => 'hma', 'Hma1.2p1_2783F.1_g328410' => 'hma', 'Hund00466' => 'sun', 'Hund03528' => 'sun', 'Hund14675' => 'sun', 'Hund18400' => 'sun', 'Hund18423' => 'sun', 'Hund20459' => 'sun', 'Hund22182' => 'sun', 'Hund23722' => 'sun', 'Hund23891' => 'sun', 'Hund24773' => 'sun', 'Hund25597' => 'sun', 'Hund25737' => 'sun', 'Hund26483' => 'sun', 'MELO3C000149.2' => 'cme', 'MELO3C000175.2' => 'cme', 'MELO3C000447.2' => 'cme', 'MELO3C000457.2' => 'cme', 'MELO3C000787.2' => 'cme', 'MELO3C000795.2' => 'cme', 'MELO3C000923.2' => 'cme', 'MELO3C005191.2' => 'cme', 'MELO3C008788.2' => 'cme', 'MELO3C008852.2' => 'cme', 'MELO3C010339.2' => 'cme', 'MELO3C010610.2' => 'cme', 'MELO3C014196.2' => 'cme', 'MELO3C014207.2' => 'cme', 'MELO3C018936.2' => 'cme', 'MELO3C019586.2' => 'cme', 'MELO3C019765.2' => 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'cme', 'MELO3C032556.2' => 'cme', 'MELO3C032588.2' => 'cme', 'MELO3C032941.2' => 'cme', 'MELO3C033114.2' => 'cme', 'MELO3C033120.2' => 'cme', 'MELO3C033121.2' => 'cme', 'MELO3C034058.2' => 'cme', 'MELO3C034076.2' => 'cme', 'MELO3C034118.2' => 'cme', 'MELO3C034125.2' => 'cme', 'MELO3C034172.2' => 'cme', 'MELO3C034175.2' => 'cme', 'MELO3C034272.2' => 'cme', 'MELO3C034677.2' => 'cme', 'MELO3C034692.2' => 'cme', 'MELO3C035479.2' => 'cme', 'MELO3C035500.2' => 'cme', 'MELO3C035510.2' => 'cme', 'MELO3C035511.2' => 'cme', 'MSTRG.1983' => 'ama', 'MSTRG.26045' => 'ama', 'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' => 'cqu', 'AUR62037974' => 'cqu', 'AUR62042503' => 'cqu', 'AUR62043964' => 'cqu', 'CAN.G1088.3' => 'can', 'CAN.G1130.7' => 'can', 'CAN.G1360.3' => 'can', 'CAN.G1525.6' => 'can', 'CAN.G27.12' => 'can', 'CAN.G322.132' => 'can', 'CAN.G536.2' => 'can', 'CAN.G58.39' => 'can', 'CAN.G624.18' => 'can', 'CAN.G884.20' => 'can', 'CAN.G959.8' => 'can', 'ClCG01G008450' => 'cla', 'ClCG01G008830' => 'cla', 'ClCG01G008840' => 'cla', 'ClCG01G009740' => 'cla', 'ClCG01G012490' => 'cla', 'ClCG01G016350' => 'cla', 'ClCG02G007050' => 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'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ), 'gf_id' => 'HOM05D000995', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D000995' ), 'data_identifier' => 'HOM05D000995', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D000995', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '608', 'num_species' => '25' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AUR62015264' => 'cqu', 'AUR62015265' => 'cqu', 'AUR62015266' => 'cqu', 'AUR62025802' => 'cqu', 'AUR62025930' => 'cqu', 'AUR62026535' => 'cqu', 'AUR62027594' => 'cqu', 'AUR62034805' => 'cqu', 'AUR62036109' => 'cqu', 'AUR62036110' => 'cqu', 'AUR62036388' => 'cqu', 'AUR62036389' 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'MSTRG.26889' => 'ama', 'Nitab4.5_0000003g0300' => 'nta', 'Nitab4.5_0000022g0410' => 'nta', 'Nitab4.5_0000022g0420' => 'nta', 'Nitab4.5_0000032g0300' => 'nta', 'Nitab4.5_0000055g0190' => 'nta', 'Nitab4.5_0000059g0150' => 'nta', 'Nitab4.5_0000109g0010' => 'nta', 'Nitab4.5_0000199g0110' => 'nta', 'Nitab4.5_0000378g0120' => 'nta', 'Nitab4.5_0000378g0130' => 'nta', 'Nitab4.5_0000481g0130' => 'nta', 'Nitab4.5_0000639g0150' => 'nta', 'Nitab4.5_0002941g0030' => 'nta', 'Nitab4.5_0002941g0050' => 'nta', 'Nitab4.5_0003624g0070' => 'nta', 'Nitab4.5_0004620g0050' => 'nta', 'Nitab4.5_0007746g0040' => 'nta', 'Nitab4.5_0010291g0010' => 'nta', 'Nitab4.5_0010513g0020' => 'nta', 'Nitab4.5_0022154g0010' => 'nta', 'PGSC0003DMG400001285' => 'stu', 'PGSC0003DMG400007485' => 'stu', 'PGSC0003DMG400009586' => 'stu', 'PGSC0003DMG400013728' => 'stu', 'PGSC0003DMG400015099' => 'stu', 'PGSC0003DMG400015915' => 'stu', 'PGSC0003DMG400018021' => 'stu', 'PGSC0003DMG400018974' => 'stu', 'PGSC0003DMG400020615' => 'stu', 'PGSC0003DMG400023003' => 'stu', 'PGSC0003DMG400030152' => 'stu', 'PGSC0003DMG400031332' => 'stu', 'PGSC0003DMG400034797' => 'stu', 'PGSC0003DMG400035210' => 'stu', 'PGSC0003DMG400035791' => 'stu', 'PGSC0003DMG400036228' => 'stu', 'PGSC0003DMG400038482' => 'stu', 'PGSC0003DMG400040325' => 'stu', 'PGSC0003DMG400042344' => 'stu', 'PGSC0003DMG400043966' => 'stu', 'PGSC0003DMG400044289' => 'stu', 'PGSC0003DMG400044720' => 'stu', 'PGSC0003DMG400044879' => 'stu', 'PGSC0003DMG400046252' => 'stu', 'PGSC0003DMG400046895' => 'stu', 'QL01p032001' => 'qlo', 'QL02p003670' => 'qlo', 'QL02p080036' => 'qlo', 'QL03p031177' => 'qlo', 'QL03p037625' => 'qlo', 'QL04p030586' => 'qlo', 'QL04p075038' => 'qlo', 'QL04p075594' => 'qlo', 'QL05p007927' => 'qlo', 'QL05p018402' => 'qlo', 'QL05p048948' => 'qlo', 'QL06p019608' => 'qlo', 'QL07p006782' => 'qlo', 'QL07p015633' => 'qlo', 'QL07p017318' => 'qlo', 'QL08p015694' => 'qlo', 'QL08p038287' => 'qlo', 'QL09p024406' => 'qlo', 'QL09p028511' => 'qlo', 'QL10p017437' => 'qlo', 'QL10p026410' => 'qlo', 'QL11p006726' => 'qlo', 'QL11p025177' => 'qlo', 'QL11p054594' => 'qlo', 'QL93p0181_0012' => 'qlo', 'QL93p0209_0006' => 'qlo', 'Rhsim01G0078000' => 'rsi', 'Rhsim01G0099100' => 'rsi', 'Rhsim01G0104900' => 'rsi', 'Rhsim01G0139000' => 'rsi', 'Rhsim02G0072700' => 'rsi', 'Rhsim02G0098200' => 'rsi', 'Rhsim02G0113000' => 'rsi', 'Rhsim02G0146600' => 'rsi', 'Rhsim02G0153100' => 'rsi', 'Rhsim02G0154400' => 'rsi', 'Rhsim02G0167000' => 'rsi', 'Rhsim02G0187300' => 'rsi', 'Rhsim03G0094500' => 'rsi', 'Rhsim04G0169400' => 'rsi', 'Rhsim05G0112600' => 'rsi', 'Rhsim05G0131300' => 'rsi', 'Rhsim05G0140400' => 'rsi', 'Rhsim05G0147000' => 'rsi', 'Rhsim07G0168400' => 'rsi', 'Rhsim07G0182500' => 'rsi', 'Rhsim08G0105700' => 'rsi', 'Rhsim08G0105800' => 'rsi', 'Rhsim08G0106900' => 'rsi', 'Rhsim08G0107300' => 'rsi', 'Rhsim09G0065400' => 'rsi', 'Rhsim11G0065300' => 'rsi', 'Rhsim11G0065400' => 'rsi', 'Rhsim11G0143600' => 'rsi', 'Rhsim13G0131600' => 'rsi', 'RhsimUnG0218100' => 'rsi', 'SalBow2G3402' => 'sbo', 'SalBow5G0102' => 'sbo', 'SalBow5G0405' => 'sbo', 'SalBow5G1216' => 'sbo', 'SalBow5G1967' => 'sbo', 'SalBow6G5430' => 'sbo', 'SalBow8G2838' => 'sbo', 'Sc04g0005820' => 'sci', 'Sc08g0003050' => 'sci', 'Sc23g0003830' => 'sci', 'Sed0007114' => 'sed', 'Sed0007388' => 'sed', 'Sed0008092' => 'sed', 'Sed0013325' => 'sed', 'Sed0014458' => 'sed', 'Sed0015617' => 'sed', 'Sed0017387' => 'sed', 'Sed0018066' => 'sed', 'Sed0018372' => 'sed', 'Sed0019125' => 'sed', 'Sed0019276' => 'sed', 'Sed0020039' => 'sed', 'Sed0021058' => 'sed', 'Sed0026097' => 'sed', 'Sed0027461' => 'sed', 'SGA_v2.0_scaffold352G49690' => 'sas', 'Solyc04g048905.1' => 'sly', 'Solyc09g018215.1' => 'sly', 'Sopen05g021300' => 'spe', 'Sopen06g006570' => 'spe', 'Sopen09g017340' => 'spe', 'Sopen10g011360' => 'spe', 'TAR369G0964' => 'tar', 'TAR381G0220' => 'tar', 'TAR383G0832' => 'tar', 'TAR383G0882' => 'tar', 'TAR625G0284' => 'tar', 'TAR633G1924' => 'tar', 'TAR636G0961' => 'tar', 'TAR636G2706' => 'tar', 'TAR636G2900' => 'tar', 'TWI18G0122' => 'twi', 'TWI23G1272' => 'twi', 'TWI53G1702' => 'twi', 'TWI60G0990' => 'twi', 'TWI60G1262' => 'twi', 'TWI77G0479' => 'twi', 'TWI77G0552' => 'twi', 'TWI79G1589' => 'twi' ) $gf_id = 'HOM05D000995' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D000995' ) $data_identifier = 'HOM05D000995' $data_type = 'gf_id' $species_gene_counts = array( 'cqu' => (int) 15, 'can' => (int) 11, 'cla' => (int) 35, 'csa' => (int) 1, 'camsi' => (int) 7, 'din' => (int) 1, 'bvu' => (int) 26, 'fan' => (int) 250, 'fve' => (int) 12, 'hma' => (int) 11, 'sun' => (int) 13, 'cme' => (int) 73, 'ama' => (int) 3, 'nta' => (int) 20, 'stu' => (int) 25, 'qlo' => (int) 26, 'rsi' => (int) 30, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 15, 'sas' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 4, 'tar' => (int) 9, 'twi' => (int) 8 ) $gf_gene_species = 'twi' $gf_gene_id = 'TWI79G1589' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1